Re: [AMBER] internal geometry restraint

From: Jio M <>
Date: Thu, 28 Nov 2013 07:40:28 -0800 (PST)

Dear David and Jason

I tried a test case with explicit waters with input as follows: (I wish it soon gets implemented with pmemd.MPI)
mpirun -np 8 sander.MPI -O -i -o emap.out -c final.rst -p a.prmtop -r emap.rst -x emap.trj

***** input****
&cntrl (part removed)

  mapfile='del.pdb',atmask=':1-10,11-20',fcons=1, ## one structure in del.pdb; can be 1-20
  mapfit='',molfit='', /
  mapfile='del.pdb',atmask=':21-30,31-40',fcons=1, ## second structure in del.pdb; can be 21-40
  mapfit='',molfit='', /

It looks like working fine as I can see in trajectory, please let me know if I have understood it correctly:

1) This will consider interaction between two rigid bodies (1 to 20 and 21 to 40)

2) The mapfile which I have used is pdb file (del.pdb; without ions and
waters). This input will try to keep internal geometry rigid according
to structure defined in del.pdb (thus this del.pdb must be obtained from starting prmtop and inpcrd/restart)

3) I am not sure about ifit flag (default ifit=0). Lets say if I use
starting simulation structure (rst file) different from mapfile then I
should use ifit =1? But in my case del.pdb which is obtained from prmtop and rst itself so ifit =0 seems ok.

4) Again I just need restart file from this simulation to perform further
simulations without retsraints simulations so no need to provide mapfit
and molfit

5) grid again kept default; honestly not sure about this grid fitting, can default values be considered as 'ideal value'? In order to keep
internal geometry strictly according to mapfit (del.pdb) which one should be
changed: fcons or grid? (I tried increasing fcons to 10 and I get vlimit error; keeping fcons=1 more or less works fine anyhow)

thanks and kind regards,Jiomm

On Tuesday, November 26, 2013 10:56 PM, case <> wrote:

On Tue, Nov 26, 2013, Jio M wrote:

> I have three linear polymers and I have placed them parallel to each
> other. I am not sure they have been placed 'very close' because my
> script just considered the atoms as point coordinates while placing
> them. So when I run a simulation they are repelled to each other in
> just 50 ps and the internal geometry of each polymer chain is destroyed
> badly.

> What I am thinking is to run first some simulation considering three
> polymer chains as 'hard rods', that is keeping internal geometry
> coordinates of a polymer constrained (all atoms in a polymer chain being
> fixed with respect to each other; keeping internal geometry of polymer
> chain fixed) so that they just act as hard rods and can adjust their
> positions and later I release the restraints.

You can carry out a version of this sort of calculation using "EMAP"
constraints, as explained in section 6.13 of the manual.  This is not exactly
what you describe, but it might suffice.  You'll probably have to experiment a
bit (or a lot!) with force constants and the resolution of the maps you are
using.  Some other dynamics programs do a better job of allowing you to define
rigid groups that can move relative to each other.


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Received on Thu Nov 28 2013 - 08:00:02 PST
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